| Calling Sequence | BootstrapTree(Ds,labels,bstype)
BootstrapTree(Ds,labels,nrounds,bstype) BootstrapTree(treeofall,bstrees,bstype) | ||||||||||||||||||||||||
| Parameters |
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| Return Type | Tree | ||||||||||||||||||||||||
| Synopsis | Depending on the value of 'bstype', this function computes confidence values for internal nodes (default) or branches. The values are integers between 0 and 100, denoting how often (in percent) a particular node or branch occured during the bootstrapping. By default, 100 bootstrapping trees from randomly selected distance matrices (prob 2/3) are constructed and evaluated. Typically, each of the input matrices corresponds to one orthologous group. Alternatively, a tree from all data plus a list of trees from bootstrapping experiments could be given as arguments. The confidence values are stored in the fourth field of the Tree data structure and can be displayed using the option InternalNodes = ShowBootstrap or BranchDrawing = ShowBootstrap for the DrawTree function. To make the result more readable, only bootstrap values below 100 percent are displayed. | ||||||||||||||||||||||||
| Examples | > T1 := Tree(Tree(Tree(Leaf('A',-3),-2,Leaf('B',-3) ),-1,Leaf('C',-3)),0,
Tree(Tree(Leaf('E',-3),-2,Leaf('F',-3) ),-1,Leaf('D',-3))):
> T2 := Tree(Tree(Tree(Leaf('B',-3),-2,Leaf('C',-3) ),-1,Leaf('A',-3)),0,
Tree(Tree(Leaf('D',-3),-2,Leaf('E',-3) ),-1,Leaf('F',-3))):
> BS1 := BootstrapTree(T1, [T1,T2]); BS1 := Tree(Tree(Tree(Leaf(A,-3),-2,Leaf(B,-3),50),-1,Leaf(C,-3),50),0,Tree(Tree (Leaf(E,-3),-2,Leaf(F,-3),50),-1,Leaf(D,-3),50)) > DrawTree(BS1, InternalNodes=ShowBootstrap); > BS2 := BootstrapTree(T1, [T1,T2], Branches); BS2 := Tree(Tree(Tree(Leaf(A,-3),-2,Leaf(B,-3),50),-1,Leaf(C,-3),100),0,Tree(Tre e(Leaf(E,-3),-2,Leaf(F,-3),50),-1,Leaf(D,-3),100)) > DrawTree(BS2, BranchDrawing=ShowBootstrap); | ||||||||||||||||||||||||
| See also | ComputeDimensionlessFit, DrawTree, LeastSquaresTree, PhylogeneticTree, RBFS_Tree, Tree | ||||||||||||||||||||||||